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authorKen Kellner <ken@kenkellner.com>2019-02-13 21:36:23 (GMT)
committerKen Kellner <ken@kenkellner.com>2019-02-13 21:36:23 (GMT)
commit95bc79786d33981b107f0777a0cf9e120fd5780d (patch)
tree2f0fe63aa156739c08b2b154a1bf82ea7ccf3fdf
parent6d741817f89bbb60fca2bbf8b6d13488bddbfd6f (diff)
Start updating appendix 2 with better names
-rw-r--r--supplements/appendixS2.Rmd248
-rw-r--r--supplements/appendixS2_old.Rmd254
2 files changed, 335 insertions, 167 deletions
diff --git a/supplements/appendixS2.Rmd b/supplements/appendixS2.Rmd
index c663d06..e35b727 100644
--- a/supplements/appendixS2.Rmd
+++ b/supplements/appendixS2.Rmd
@@ -17,7 +17,7 @@ source('.Rprofile')
**Table S2.2**. Mammal species included in analyses and matching index values.
```{r,echo=F}
-mam.sp <- read.csv('lvl1/mam_species.csv',header=T)
+mam.sp <- read.csv(outpath('tableS2_lvl1/mam_species.csv'),header=T)
names(mam.sp) <- c('Index','Code','Species Name')
knitr::kable(mam.sp)
```
@@ -25,7 +25,7 @@ knitr::kable(mam.sp)
**Table S2.3**. Bat species included in analyses and matching index values.
```{r,echo=F}
-bats.sp <- read.csv('lvl1/bat_species.csv',header=T)
+bats.sp <- read.csv(outpath('tableS2_lvl1/bat_species.csv'),header=T)
names(bats.sp) <- c('Index','Code','Species Name')
knitr::kable(bats.sp)
```
@@ -35,7 +35,7 @@ knitr::kable(bats.sp)
**Table S2.4**. Bird species included in analyses and matching index values.
```{r,echo=F}
-bird.sp <- read.csv('lvl1/bird_species.csv',header=T)
+bird.sp <- read.csv(outpath('tableS2_lvl1/bird_species.csv'),header=T)
names(bird.sp) <- c('Index','Code','Species Name')
knitr::kable(bird.sp)
```
@@ -45,199 +45,113 @@ knitr::kable(bird.sp)
**Table S2.5**. Aquatic turtle species included in analyses and matching index values.
```{r,echo=F}
-turtle.sp <- read.csv('lvl1/turtle_species.csv',header=T)
+turtle.sp <- read.csv(outpath('tableS2_lvl1/turtle_species.csv'),header=T)
names(turtle.sp) <- c('Index','Code','Species Name')
knitr::kable(turtle.sp)
```
# Level-1 Analysis Output (Individual Plot Scale)
-**Table S2.6**. Output from multi-species plot-level occupancy model for small mammals. See Table S2.2 for species indices.
-
-```{r,echo=F}
-inp <- read.csv('lvl1/mam_lvl1.csv',header=T)
-inp <- cbind(inp[,1],round(inp[,2:7],2))
-names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
-knitr::kable(inp)
-```
-
-**Table S2.7**. Output from multi-species plot-level occupancy model for bats. See Table S2.3 for species indices.
-
-```{r,echo=F}
-inp <- read.csv('lvl1/bat_lvl1.csv',header=T)
-inp <- cbind(inp[,1],round(inp[,2:7],2))
-names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
-knitr::kable(inp)
-```
-
-**Table S2.8**. Output from multi-species plot-level occupancy model for birds. See Table S2.4 for species indices.
-
-```{r,echo=F}
-inp <- read.csv('lvl1/bird_lvl1.csv',header=T)
-inp <- cbind(inp[,1],round(inp[,2:7],2))
-names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
-knitr::kable(inp)
-```
-
-**Table S2.9**. Output from multi-species plot-level occupancy model for aquatic turtles. See Table S2.5 for species indices.
-
-```{r,echo=F}
-inp <- read.csv('lvl1/turtle_lvl1.csv',header=T)
-inp <- cbind(inp[,1],round(inp[,2:7],2))
-names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
-knitr::kable(inp)
-```
-
-# Level-2 Analysis Output (Landscape Scale)
-
-## Small Mammals
-
-**Table S2.10**. Output from model NN (no imperfect detection, no phylogenetic relationships) for small mammals. See Table S2.2 for species indices.
-
-```{r,echo=F}
-inp <- read.csv('lvl2/mam_NN.csv',header=T)
-inp <- cbind(inp[,1],round(inp[,2:7],2))
-names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
-knitr::kable(inp)
-```
-
-**Table S2.11**. Output from model IN (imperfect detection, no phylogenetic relationships) for small mammals. See Table S2.2 for species indices.
-
-```{r,echo=F}
-inp <- read.csv('lvl2/mam_IN.csv',header=T)
-inp <- cbind(inp[,1],round(inp[,2:7],2))
-names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
-knitr::kable(inp)
-```
-
-**Table S2.12**. Output from model NP (no imperfect detection, phylogenetic relationships) for small mammals. See Table S2.2 for species indices.
-
-```{r,echo=F}
-inp <- read.csv('lvl2/mam_NP.csv',header=T)
-inp <- cbind(inp[,1],round(inp[,2:7],2))
-names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
-knitr::kable(inp)
-```
-
-**Table S2.13**. Output from model IP (imperfect detection, phylogenetic relationships) for small mammals. See Table S2.2 for species indices.
-
```{r,echo=F}
-inp <- read.csv('lvl2/mam_IP.csv',header=T)
-inp <- cbind(inp[,1],round(inp[,2:7],2))
-names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
-knitr::kable(inp)
+suppressMessages(library(tidyverse))
```
-## Bats
-
-**Table S2.14**. Output from model NN (no imperfect detection, no phylogenetic relationships) for bats. See Table S2.3 for species indices.
+**Table S2.6**. Output from multi-species plot-level occupancy model for small mammals. Species indices are in brackets (see Table S2.2).
```{r,echo=F}
-inp <- read.csv('lvl2/bat_NN.csv',header=T)
-inp <- cbind(inp[,1],round(inp[,2:7],2))
-names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
-knitr::kable(inp)
-```
+inp <- read.csv(outpath('tableS2_lvl1/mam_lvl1.csv'),header=T)
+inp <- cbind(inp[,1],round(inp[,c(2,4,5,6)],2))
+names(inp) <- c('Parameter','Mean','2.5%','97.5%','f')
-**Table S2.15**. Output from model IN (imperfect detection, no phylogenetic relationships) for bats. See Table S2.3 for species indices.
+inp_out <- inp %>%
+ filter(!str_detect(Parameter,'pmean'),!str_detect(Parameter,'psimean'),
+ !str_detect(Parameter,'deviance'))
-```{r,echo=F}
-inp <- read.csv('lvl2/bat_IN.csv',header=T)
-inp <- cbind(inp[,1],round(inp[,2:7],2))
-names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
-knitr::kable(inp)
+nspecies <- 11
+param_names <- c('Detection: Date effect','Occupancy: Intercept',
+ 'Occupancy: Grassland effect','Occupancy: Agriculture effect',
+ 'Occupancy: Corridor effect','Detection: Grassland effect',
+ 'Detection: Agriculture effect','Detection: Corridor effect')
+inp_out$Index <- rep(1:nspecies,length(param_names))
+indices <- paste('[',inp_out$Index,']',sep='')
+pn_raw <- rep(param_names,each=nspecies)
+inp_out$Parameter <- paste(pn_raw,indices,sep='')
+inp_out$pn_raw <- pn_raw
+inp_out <- inp_out %>% arrange(pn_raw,Index) %>% select(-pn_raw,-Index)
+knitr::kable(inp_out)
```
-**Table S2.16**. Output from model NP (no imperfect detection, phylogenetic relationships) for bats. See Table S2.3 for species indices.
+**Table S2.7**. Output from multi-species plot-level occupancy model for bats. Species indices are in brackets (see Table S2.3).
```{r,echo=F}
-inp <- read.csv('lvl2/bat_NP.csv',header=T)
-inp <- cbind(inp[,1],round(inp[,2:7],2))
-names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
-knitr::kable(inp)
-```
+inp <- read.csv(outpath('tableS2_lvl1/bat_lvl1.csv'),header=T)
+inp <- cbind(inp[,1],round(inp[,c(2,4,5,6)],2))
+names(inp) <- c('Parameter','Mean','2.5%','97.5%','f')
-**Table S2.17**. Output from model IP (imperfect detection, phylogenetic relationships) for bats. See Table S2.3 for species indices.
+inp_out <- inp %>%
+ filter(!str_detect(Parameter,'deviance'))
-```{r,echo=F}
-inp <- read.csv('lvl2/bat_IP.csv',header=T)
-inp <- cbind(inp[,1],round(inp[,2:7],2))
-names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
-knitr::kable(inp)
+nspecies <- 7
+param_names <- c('Occupancy: Intercept','Detection: Date effect',
+ 'Detection: Effort effect','Occupancy: Agriculture effect',
+ 'Occupancy: Grassland effect','Occupancy: Wetland effect',
+ 'Detection: Agriculture effect','Detection: Grassland effect',
+ 'Detection: Wetland effect')
+inp_out$Index <- rep(1:nspecies,length(param_names))
+indices <- paste('[',inp_out$Index,']',sep='')
+pn_raw <- rep(param_names,each=nspecies)
+inp_out$Parameter <- paste(pn_raw,indices,sep='')
+inp_out$pn_raw <- pn_raw
+inp_out <- inp_out %>% arrange(pn_raw,Index) %>% select(-pn_raw,-Index)
+knitr::kable(inp_out)
```
-## Birds
-
-**Table S2.18**. Output from model NN (no imperfect detection, no phylogenetic relationships) for birds. See Table S2.4 for species indices.
+**Table S2.8**. Output from multi-species plot-level abundance model for birds. Species indices are in brackets (see Table S2.4).
```{r,echo=F}
-inp <- read.csv('lvl2/bird_NN.csv',header=T)
-inp <- cbind(inp[,1],round(inp[,2:7],2))
-names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
-knitr::kable(inp)
-```
+inp <- read.csv(outpath('tableS2_lvl1/bird_lvl1.csv'),header=T)
+inp <- cbind(inp[,1],round(inp[,c(2,4,5,6)],2))
+names(inp) <- c('Parameter','Mean','2.5%','97.5%','f')
-**Table S2.19**. Output from model IN (imperfect detection, no phylogenetic relationships) for birds. See Table S2.4 for species indices.
+inp_out <- inp %>%
+ filter(!str_detect(Parameter,'deviance'),!str_detect(Parameter,'pavail'),
+ !str_detect(Parameter,'psimean'))
-```{r,echo=F}
-inp <- read.csv('lvl2/bird_IN.csv',header=T)
-inp <- cbind(inp[,1],round(inp[,2:7],2))
-names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
-knitr::kable(inp)
+nspecies <- 39
+param_names <- c('Detection: Intercept','Detection: Date effect',
+ 'Detection: Time of day effect','Abundance: Agriculture effect',
+ 'Abundance: Grassland effect','Abundance: Urban effect',
+ 'Abundance: Wetland effect','Detection: Agriculture effect',
+ 'Detection: Grassland effect','Detection: Urban effect',
+ 'Detection: Wetland effect')
+inp_out$Index <- rep(1:nspecies,length(param_names))
+indices <- paste('[',inp_out$Index,']',sep='')
+pn_raw <- rep(param_names,each=nspecies)
+inp_out$Parameter <- paste(pn_raw,indices,sep='')
+inp_out$pn_raw <- pn_raw
+inp_out <- inp_out %>% arrange(pn_raw,Index) %>% select(-pn_raw,-Index)
+knitr::kable(inp_out)
```
-**Table S2.20**. Output from model NP (no imperfect detection, phylogenetic relationships) for birds. See Table S2.4 for species indices.
+**Table S2.9**. Output from multi-species plot-level occupancy model for turtles. Species indices are in brackets (see Table S2.5).
```{r,echo=F}
-inp <- read.csv('lvl2/bird_NP.csv',header=T)
-inp <- cbind(inp[,1],round(inp[,2:7],2))
-names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
-knitr::kable(inp)
-```
-
-**Table S2.21**. Output from model IP (imperfect detection, phylogenetic relationships) for birds. See Table S2.4 for species indices.
-
-```{r,echo=F}
-inp <- read.csv('lvl2/bird_IP.csv',header=T)
-inp <- cbind(inp[,1],round(inp[,2:7],2))
-names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
-knitr::kable(inp)
-```
+inp <- read.csv(outpath('tableS2_lvl1/turtle_lvl1.csv'),header=T)
+inp <- cbind(inp[,1],round(inp[,c(2,4,5,6)],2))
+names(inp) <- c('Parameter','Mean','2.5%','97.5%','f')
-## Aquatic Turtles
+inp_out <- inp %>%
+ filter(!str_detect(Parameter,'deviance'),!str_detect(Parameter,'meanpsi'),
+ !str_detect(Parameter,'meanp'),!str_detect(Parameter,'sd'))
-**Table S2.22**. Output from model NN (no imperfect detection, no phylogenetic relationships) for turtles. See Table S2.5 for species indices.
-
-```{r,echo=F}
-inp <- read.csv('lvl2/turtle_NN.csv',header=T)
-inp <- cbind(inp[,1],round(inp[,2:7],2))
-names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
-knitr::kable(inp)
-```
-
-**Table S2.23**. Output from model IN (imperfect detection, no phylogenetic relationships) for turtles. See Table S2.5 for species indices.
-
-```{r,echo=F}
-inp <- read.csv('lvl2/turtle_IN.csv',header=T)
-inp <- cbind(inp[,1],round(inp[,2:7],2))
-names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
-knitr::kable(inp)
-```
-
-**Table S2.24**. Output from model NP (no imperfect detection, phylogenetic relationships) for turtles. See Table S2.5 for species indices.
-
-```{r,echo=F}
-inp <- read.csv('lvl2/turtle_NP.csv',header=T)
-inp <- cbind(inp[,1],round(inp[,2:7],2))
-names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
-knitr::kable(inp)
-```
-
-**Table S2.25**. Output from model IP (imperfect detection, phylogenetic relationships) for turtles. See Table S2.5 for species indices.
-
-```{r,echo=F}
-inp <- read.csv('lvl2/turtle_IP.csv',header=T)
-inp <- cbind(inp[,1],round(inp[,2:7],2))
-names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
-knitr::kable(inp)
+nspecies <- 8
+param_names <- c('Detection: Intercept','Occupancy: Intercept',
+ 'Detection: Date effect','Detection: Effort effect')
+inp_out$Index <- rep(1:nspecies,length(param_names))
+indices <- paste('[',inp_out$Index,']',sep='')
+pn_raw <- rep(param_names,each=nspecies)
+inp_out$Parameter <- paste(pn_raw,indices,sep='')
+inp_out$pn_raw <- pn_raw
+inp_out <- inp_out %>% arrange(pn_raw,Index) %>% select(-pn_raw,-Index)
+knitr::kable(inp_out)
```
diff --git a/supplements/appendixS2_old.Rmd b/supplements/appendixS2_old.Rmd
new file mode 100644
index 0000000..7e04f7d
--- /dev/null
+++ b/supplements/appendixS2_old.Rmd
@@ -0,0 +1,254 @@
+---
+title: "Appendix S2"
+output: pdf_document
+---
+
+Supplemental information for:
+
+Kellner, K. F., Duchamp, J. E., & Swihart R. K. Niche breadth and vertebrate sensitivity to habitat modification: signals from multiple taxa across replicated landscapes. Diversity & Distributions.
+
+```{r, echo=FALSE, warning=FALSE, message=FALSE}
+setwd('..')
+source('.Rprofile')
+```
+
+# Species Index
+
+**Table S2.2**. Mammal species included in analyses and matching index values.
+
+```{r,echo=F}
+mam.sp <- read.csv(outpath('tableS2_lvl1/mam_species.csv'),header=T)
+names(mam.sp) <- c('Index','Code','Species Name')
+knitr::kable(mam.sp)
+```
+
+**Table S2.3**. Bat species included in analyses and matching index values.
+
+```{r,echo=F}
+bats.sp <- read.csv(outpath('tableS2_lvl1/bat_species.csv'),header=T)
+names(bats.sp) <- c('Index','Code','Species Name')
+knitr::kable(bats.sp)
+```
+
+\pagebreak
+
+**Table S2.4**. Bird species included in analyses and matching index values.
+
+```{r,echo=F}
+bird.sp <- read.csv(outpath('tableS2_lvl1/bird_species.csv'),header=T)
+names(bird.sp) <- c('Index','Code','Species Name')
+knitr::kable(bird.sp)
+```
+
+\pagebreak
+
+**Table S2.5**. Aquatic turtle species included in analyses and matching index values.
+
+```{r,echo=F}
+turtle.sp <- read.csv(outpath('tableS2_lvl1/turtle_species.csv'),header=T)
+names(turtle.sp) <- c('Index','Code','Species Name')
+knitr::kable(turtle.sp)
+```
+
+# Level-1 Analysis Output (Individual Plot Scale)
+
+```{r,echo=F}
+suppressMessages(library(tidyverse))
+rename_params <- function(x){
+ ip <- as.character(x$Parameter)
+ op <- case_when(str_detect(ip,'pmean') ~ str_replace(ip,'pmean','Mean detect (p)'),
+ str_detect(ip,'psimean') ~ str_replace(ip,'psimean','Mean occ (psi)'),
+ str_detect(ip,'beta.date') ~ str_replace(ip,'beta.date','Date effect on p'))
+}
+```
+
+
+**Table S2.6**. Output from multi-species plot-level occupancy model for small mammals. See Table S2.2 for species indices.
+
+```{r,echo=F}
+inp <- read.csv(outpath('tableS2_lvl1/mam_lvl1.csv'),header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+**Table S2.7**. Output from multi-species plot-level occupancy model for bats. See Table S2.3 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl1/bat_lvl1.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+**Table S2.8**. Output from multi-species plot-level occupancy model for birds. See Table S2.4 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl1/bird_lvl1.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+**Table S2.9**. Output from multi-species plot-level occupancy model for aquatic turtles. See Table S2.5 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl1/turtle_lvl1.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+# Level-2 Analysis Output (Landscape Scale)
+
+## Small Mammals
+
+**Table S2.10**. Output from model NN (no imperfect detection, no phylogenetic relationships) for small mammals. See Table S2.2 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/mam_NN.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+**Table S2.11**. Output from model IN (imperfect detection, no phylogenetic relationships) for small mammals. See Table S2.2 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/mam_IN.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+**Table S2.12**. Output from model NP (no imperfect detection, phylogenetic relationships) for small mammals. See Table S2.2 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/mam_NP.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+**Table S2.13**. Output from model IP (imperfect detection, phylogenetic relationships) for small mammals. See Table S2.2 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/mam_IP.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+## Bats
+
+**Table S2.14**. Output from model NN (no imperfect detection, no phylogenetic relationships) for bats. See Table S2.3 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/bat_NN.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+**Table S2.15**. Output from model IN (imperfect detection, no phylogenetic relationships) for bats. See Table S2.3 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/bat_IN.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+**Table S2.16**. Output from model NP (no imperfect detection, phylogenetic relationships) for bats. See Table S2.3 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/bat_NP.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+**Table S2.17**. Output from model IP (imperfect detection, phylogenetic relationships) for bats. See Table S2.3 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/bat_IP.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+## Birds
+
+**Table S2.18**. Output from model NN (no imperfect detection, no phylogenetic relationships) for birds. See Table S2.4 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/bird_NN.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+**Table S2.19**. Output from model IN (imperfect detection, no phylogenetic relationships) for birds. See Table S2.4 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/bird_IN.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+**Table S2.20**. Output from model NP (no imperfect detection, phylogenetic relationships) for birds. See Table S2.4 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/bird_NP.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+**Table S2.21**. Output from model IP (imperfect detection, phylogenetic relationships) for birds. See Table S2.4 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/bird_IP.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+## Aquatic Turtles
+
+**Table S2.22**. Output from model NN (no imperfect detection, no phylogenetic relationships) for turtles. See Table S2.5 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/turtle_NN.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+**Table S2.23**. Output from model IN (imperfect detection, no phylogenetic relationships) for turtles. See Table S2.5 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/turtle_IN.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+**Table S2.24**. Output from model NP (no imperfect detection, phylogenetic relationships) for turtles. See Table S2.5 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/turtle_NP.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```
+
+**Table S2.25**. Output from model IP (imperfect detection, phylogenetic relationships) for turtles. See Table S2.5 for species indices.
+
+```{r,echo=F}
+inp <- read.csv('lvl2/turtle_IP.csv',header=T)
+inp <- cbind(inp[,1],round(inp[,2:7],2))
+names(inp) <- c('Parameter','Mean','SD','2.5%','50%','97.5%','f')
+knitr::kable(inp)
+```